example_bootstrap_results: Example bootstrap enrichment results

In NathanSkene/EWCE: Expression Weighted Celltype Enrichment

Example bootstrap enrichment results

Description

Example cell type enrichment results produced by bootstrap_enrichment_test.

Usage

example_bootstrap_results(verbose = TRUE, localHub = FALSE)

Arguments

verbose	Print messages.
localHub	If working offline, add argument localHub=TRUE to work with a local, non-updated hub; It will only have resources available that have previously been downloaded. If offline, Please also see BiocManager vignette section on offline use to ensure proper functionality.

Value

List with 3 items.

Source

# Load the single cell data

ctd <- ewceData::ctd()

# Set the parameters for the analysis

# Use 3 bootstrap lists for speed, for publishable analysis use >=10,000

reps <- 3

# Load gene list from Alzheimer's disease GWAS

example_genelist <- ewceData::example_genelist()

# Bootstrap significance test, no control for transcript length or GC content

full_results <- EWCE::bootstrap_enrichment_test( sct_data = ctd, hits = example_genelist, reps = reps, annotLevel = 1, sctSpecies = "mouse", genelistSpecies = "human" )

bootstrap_results <- full_results

save(bootstrap_results,file = "inst/extdata/bootstrap_results.rda")

Examples

full_results <- example_bootstrap_results()

NathanSkene/EWCE documentation built on April 10, 2024, 1:02 a.m.